1. New resources and strategies for genome-wide mapping in sorghum Geoff Morris Research Assistant Professor Kresovich Lab University of South Carolina

2. Why do we need gene-resolution mapping (or causal variants)? More accurate marker-assisted selection, in breeding programs and from germplasm Leverage knowledge from other crops and model plant species

3. Genotyping- by-sequencing identified 265,000 SNP markers

4. An atlas of genomic variation in 1000 sorghum accessions Genetic Variation: Recombination rates:

5. Mapping genes underlying trait variation using genome-wide association studies (GWAS) * Causative A T Phenotype Tallest Taller Tall Short Shorter Shortest p < 10 -8 p = 10 -0 Quantitative trait locus (Candidate gene) Height T A Linked SNP G C C G Unlinked SNP G C G C G C G

6. GWAS reveals multiple loci controlling panicle branch length CLV1 APO1 SP1 ID1 LUG BDE1,ID1 TCP,TLK GDD 1 THE1 LOM3 DFL2 F-box protein in rice (Ikeda et al. 2005 Dev Biol) Receptor-like kinase in maize (Lunde and Hake 2009 Genetics) Peptide transporter in rice (Li et al. 2009 Plant J) Aberrant panicle organization1 ortholog Short panicle1 homolog Thick tassel dwarf1 homolog

7. Back to basics: Pigmentation

8. Testing GWAS with validated flavonoid genes The classical testa gene B2 was cloned as Tannin1 G/T polymorphism found in GBS data Positive control for GWAS in sorghum Wu et al. PNAS 2012

9. Mapping testa (presence/absence) in an association panel GLM and CMLM (K, Q+K) identify the locus but not the gene

10. Synthetic associations can prevent gene-level resolution in GWAS tan1-a allele Synthetic associations MAF=20% MAF=46% Orozco et al. 2010 Caused by multiple independent mutations in the same gene:

11. Gene-resolution mapping of Tannin1 GLM (Q) and MLM (K) do map Tannin1 precisely

12. Precise mapping of Tannin1 in recombinant inbred lines One day of scratch tests + GBS data = Precise mapping of Tannin1 Stem borer mapping population (n=263)

13. Pericarp pigmentation in the sorghum association panel Ibraheem et al. 2010 Yellow seed1 cloned by Chopra lab

14. Basal seedling (coleoptile) pigmentation mapped in a RIL Arabidopsis TT8 Maize B1

15. Adult plant pigmentation (tan vs. purple) mapped in a RIL Colocalizes with classical P locus Maps to cluster of DFR (Maize A1)

16. Lessons learned Higher-density genotyping will yield more useful mapping results Genotyping-by-sequencing gets the most out of existing investments in RILs GWAS can provide gene-resolution mapping but signals may be complex/indirect Best of both worlds: – Nested Association Mapping (NAM) – Regional Mapping (RegMap)

17. Mapping climate-associated alleles in a high-resolution global diversity panel 700,000 SNPs genotyped in 2,500 source-identified accessions of African and Asian origin

18. More info: www.morrislab.org Starting November 1 Assistant Professor Sorghum Genetics and Genomics Department of Agronomy

19. Project team University of South Carolina Stephen Kresovich, Davina Rhodes, Zachary Brenton Cornell University/Institute for Genomic Diversity/USDA-ARS SNP pipeline: Ed Buckler, Jeff Glaubitz, James Harriman Genotyping: Sharon Mitchell, Charlotte Acharya International Crops Research Institute for the Semi-Arid Tropics (ICRISAT – Patancheru, India) Punna Ramu* Germplasm: Tom Hash, Oscar Riera-Lizarazu, Hari Upadhyaya, Santosh Deshpande, Vinayan Madhumal Bioinformatics: Trushar Shah University of Illinois Phenotypes: Patrick Brown Iowa State University Jianming Yu Funding NSF/Gates-Basic Research to Enable Agricultural Development USDA-Feedstock Genomics